sssc: Same Species Sample Contamination Detection
Imports Variant Calling Format file into R. It can detect
whether a sample contains contaminant from the same species.
In the first stage of the approach, a change-point detection
method is used to identify copy number variations for filtering.
Next, features are extracted from the data for a support vector
machine model. For log-likelihood calculation, the deviation
parameter is estimated by maximum likelihood method. Using
a radial basis function kernel support vector machine, the
contamination of a sample can be detected.
| Version: |
1.0.0 |
| Depends: |
R (≥ 3.4.0) |
| Imports: |
changepoint, e1071, ggplot2, stats, VGAM |
| Published: |
2018-06-15 |
| Author: |
Tao Jiang [aut, cre] |
| Maintainer: |
Tao Jiang <tjiang8 at ncsu.edu> |
| License: |
GPL-2 |
| NeedsCompilation: |
no |
| Materials: |
README |
| CRAN checks: |
sssc results |
Documentation:
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